Even during the " Night of the long knives" the Wehrmacht Generals were involved more or less as they wanted to get rid of their rivalry, i. e. The SA. Not sure about the SS as Hitler had Heer Generals around him under pressure to be changed to more pro-Hitler individuals.
Gen. Fritz Lindemann, COG of 132nd Inf. Div. was an anti-nazi who refused to take part in "rat-clearing" ops. Transferred to staff positions in Germany and became part of the July 20th group. After the coup failed, he went into hiding, but was found by the Gestapo and shot while trying to escape. He died some days later of his wounds.
The Wehrmact and its top commanders wasn't all clean. A lot of the commanders, while not specifically targeting Jewish civilians in captures areas, were rather ruthless towards prisoners-of-war and dissidents (though maybe no worse than the Japanese.) Among the field commanders, von Manstein probably got the longest jail sentence at 18 years. Charges for most others accused were not pursued very enthusiastically. Some commanders (like von Runstedt) were just too old and derelict to stand trial.Some others were tolerated because of post-war aid given to western allies (against the USSR.)